Status of Clear Lake Hitch in Lower Blue Lake, Lake County, California
No abstract available.
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Geology topics
Frederick Feyrer
Publications and source records attributed to Frederick Feyrer.
Gillnet sampling methods for monitoring status and trends of Clear Lake Hitch in Clear Lake, Lake County, California
The Clear Lake Hitch ( Lavinia exilicauda chi ) is a minnow endemic to Clear Lake, Lake County, California. This species is listed as a threatened species under the California Endangered Species Act and has been petitioned for listing under the United States Endangered Species Act. In 2017, the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, initiated a Clear Lake Hitch monitoring program to generate information annually on relative abundance and size structure. The monitoring program was organized around a conceptual life cycle diagram, focused on life stages approximately ≥1 year of age, and incorporated a probabilistic study design involving approximately 10 days of short-duration (approximately 40 minutes) gillnet sampling undertaken during daytime. This report documents monitoring program activities from 2017 to 2023 and presents the results of an evaluation of the monitoring program. The evaluation was done after the 2023 sampling event, following 6 years of implementation, which is the approximate generation cycle of Clear Lake Hitch. The results of the evaluation indicated the following: (1) gillnets used in the monitoring program were effective at capturing Clear Lake Hitch aged 1 year or more; (2) the study design was effective at generating the information needed to characterize Clear Lake Hitch relative abundance and size structure, and meaningful operational efficiencies can be obtained by implementing simple changes; and (3) future sampling can be scaled to approximately 4–7 days of effort and maintain at least 80-percent confidence in detecting at least a 25-percent change in abundance, assuming past work productivity is maintained and future data are typical of previous data.
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An updated conceptual model of Delta Smelt biology: Our evolving understanding of an estuarine fish
The main purpose of this report is to provide an up-to-date assessment and conceptual model of factors affecting Delta Smelt (Hypomesus transpacificus) throughout its primarily annual life cycle and to demonstrate how this conceptual model can be used for scientific and management purposes. The Delta Smelt is a small estuarine fish that only occurs in the San Francisco Estuary. Once abundant, it is now rare and has been protected under the federal and California Endangered Species Acts since 1993. The Delta Smelt listing was related to a step decline in the early 1980s; however, population abundance decreased even further with the onset of the “pelagic organism decline” (POD) around 2002. A substantial, albeit short-lived, increase in abundance of all life stages in 2011 showed that the Delta Smelt population can still rebound when conditions are favorable for spawning, growth, and survival. In this report, we update previous conceptual models for Delta Smelt to reflect new data and information since the release of the last synthesis report about the POD by the Interagency Ecological Program for the San Francisco Estuary (IEP) in 2010. Specific objectives include: 1. Provide decision makers with a practical tool for evaluating difficult trade-offs associated with management and policy decisions. 2. Provide scientists with a framework from which they can formulate and evaluate hypotheses using qualitative or quantitative models. 3. Provide the general public with a new way of learning about Delta Smelt and their habitat. Our updated conceptual model describes the habitat conditions and ecosystem drivers affecting each Delta Smelt life stage, across seasons and how the seasonal effects contribute to the annual success of the species. The conceptual model consists of two nested and linked levels of increasing specificity. The general life cycle conceptual model for four Delta Smelt life stages (adults, eggs and larvae, juveniles, and subadults) includes stationary ecosystem components and dynamic environmental drivers, habitat attributes, and Delta Smelt responses. The more detailed life stage transition conceptual models for each of the four Delta Smelt life stages describe relationships between environmental drivers, key habitat attributes, and the responses of Delta Smelt to habitat attributes as they transition from one life stage to the next. Our analyses and conceptual model show that good larval recruitment is essential for setting the stage for a strong year class; however, increased growth and survival through subsequent life stages are also needed to achieve and sustain higher population abundance. We used our conceptual model to generate 16 hypotheses about the factors that may have contributed to the 2011 increase in Delta Smelt relative abundance. We then evaluated these hypotheses by comparing habitat conditions and Delta Smelt responses in the wet year 2011 to those in the prior wet year 2006 and in the drier years 2005 and 2010. Larval recruitment was similarly high in both wet years and lower in the drier antecedent years, but juvenile and adult abundance increased only in 2011. In 2005 and 2006, the population was limited by very poor survival from the larval to the juvenile life stage. We found that in 2011, Delta Smelt may have benefitted from a combination of favorable habitat conditions throughout the year, including: 1. Adults and larvae benefitted from prolonged cool spring water temperatures, high 2011 winter and spring outflows which reduced entrainment risk and possibly improved other habitat conditions, and possibly enhanced food availability in late spring. 2. Juveniles benefitted from cool water temperatures in late spring and early summer as well as from improved food availability and low levels of harmful Microcystis. 3. Subadults also benefitted from improved food availability and from favorable habitat conditions in the large, low salinity zone (salinity 1-6) located more toward Suisun Bay,
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Synthesis of studies in the fall low-salinity zone of the San Francisco Estuary, September-December 2011
In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus , a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: • To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. • To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. • To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments. The basic approach of this report is to evaluate predictions derived from the hypotheses included in the conceptual model developed within the adaptive management plan. All available data from studies and monitoring conducted in fall 2011 and similar data from fall 2006, which was the most recent wet year preceding 2011, were considered. Data from 2005 and 2010 were also considered, to include the conditions antecedent to those years. Many of the predictions either could not be evaluated with the data available, or the needed data were not collected. Most of the predictions that could be addressed involved either the abiotic habitat components (that is, the physical environment) or delta smelt responses. In general, the fall low-salinity habitat investigation has been largely inconclusive as of the writing of this report. This is not to be unexpected in the first year of what is intended to be a multi-year adaptive-management effort. This report can be viewed as the first chapter of a “living document” that is to be continually updated as part of the adaptive management cycle. The results of this report, especially predictions with insufficient data for evaluation, indicate a number of science-based approaches to improve the fall low-salinity habitat investigations: • Develop a method of measuring “hydrodynamic complexity.” This concept is central to a number of the predictions that could not be evaluated. • Determine if wind speed warrants a stand-alone prediction. The wind-speed prediction is directly related to the turbidity predictions, and wind is only one of several factors important for determining turbidity. • Determine the correct spatial and temporal scale or scales necessary for monitoring and for studies to address the predicted abiotic and biotic responses. Many of the assessments in this report were based on monthly sampling of dynamic habitat components, such as phytoplankton and zooplankton populations, that can change on daily scales. • Address the nutrient predictions as part of developing a phytoplankton production model that includes nutrient cycling and other important processes, if feasible. At a minimum develop a mechanistic conceptual model to support more processed-based interpretations of data or design of new studies, rather than making simple predictions of increase or decrease. • Determine if studies of predation rates are feasible in areas where there are delta smelt.
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Implications for future survival of delta smelt from four climate change scenarios for the Sacramento–San Joaquin Delta, California
Changes in the position of the low salinity zone, a habitat suitability index, turbidity, and water temperature modeled from four 100-year scenarios of climate change were evaluated for possible effects on delta smelt Hypomesus transpacificus , which is endemic to the Sacramento–San Joaquin Delta. The persistence of delta smelt in much of its current habitat into the next century appears uncertain. By mid-century, the position of the low salinity zone in the fall and the habitat suitability index converged on values only observed during the worst droughts of the baseline period (1969–2000). Projected higher water temperatures would render waters historically inhabited by delta smelt near the confluence of the Sacramento and San Joaquin rivers largely uninhabitable. However, the scenarios of climate change are based on assumptions that require caution in the interpretation of the results. Projections like these provide managers with a useful tool for anticipating long-term challenges to managing fish populations and possibly adapting water management to ameliorate those challenges.
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Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary
We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, California, USA, over 40 years using Bayesian change point models. Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). We coupled Bayesian model selection with linear regression splines to identify biotic or abiotic covariates with the strongest associations with abundances of each species. We then refitted change point models conditional on the selected covariates to explore whether those covariates could explain statistical trends or change points in species abundances. We also fitted a multispecies change point model that identified change points common to all species. All models included hierarchical structures to model data uncertainties, including observation errors and missing covariate values. There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2 isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species' abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.
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Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)
Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt ( Hypomesus transpacificus ), longfin smelt ( Spirinchus thaleichthys ), striped bass ( Morone saxatilis ), and threadfin shad ( Dorosoma petenense ). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2 isohaline (a measure of the physical response of the estuary to freshwater flow) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock–recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state–space models that describe more fully the life-history dynamics of the declining species.
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